Hi all, I was analyzing my data using MS-GF+ and then converted its output .mzid to .pepXML using idconvert. Then I tried to analyze them using Peptideprophet of the TPP GUI 'Petunia'. I choose the Pipeline- Tandem. Then it is not showing the files, so I converted the .pepXML files to .XML format by using "save as" option in notepad. I have three files. After that I ran those files again on Peptideprophet of the TPP GUI 'Petunia'. But following error message is appearing. I also used the non-parametric model during analysis.
C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 (Windows_NT-x86_64)) PPM mode in Accurate Mass Model ... running: "C:/TPP/bin/InteractParser "/tmp/a02972/params/MS-GF/interact.pep.xml" "PQC1_Q1.XML" "PQC1_Q2.XML" "PQC1_Q3.XML" -L"7"" file 1: PQC1_Q1.XMLWARNING: empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzML in msms_run_summary tag... trying .mzXML ...WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzXML in msms_run_summary tag...WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzML in msms_run_summary tag... trying .mzXML ...WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q1.mzXML in msms_run_summary tag... file 2: PQC1_Q2.XMLWARNING: empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzML in msms_run_summary tag... trying .mzXML ...WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzXML in msms_run_summary tag...WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzML in msms_run_summary tag... trying .mzXML ...WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q2.mzXML in msms_run_summary tag... file 3: PQC1_Q3.XMLWARNING: empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzML in msms_run_summary tag... trying .mzXML ...WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzXML in msms_run_summary tag...WARNING: empty raw_data in msms_run_summary tag... trying .mzML ...WARNING: cannot open data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzML in msms_run_summary tag... trying .mzXML ...WARNING: CANNOT correct data file c:/TPP/data/params/MS-GF/PQC1_Q3.mzXML in msms_run_summary tag... processed altogether 13489 results INFO: Results written to file: /tmp/a02972/params/MS-GF/interact.pep.xml command completed in 6 sec running: "C:/TPP/bin/DatabaseParser "/tmp/a02972/params/MS-GF/interact.pep.xml""command completed in 0 sec running: "C:/TPP/bin/RefreshParser "/tmp/a02972/params/MS-GF/interact.pep.xml" "C:\MS-GF\Human.fasta"" - Searching the tree... - Linking duplicate entries... - Printing results... - Building Commentz-Walter keyword tree...command completed in 4 sec running: "C:/TPP/bin/PeptideProphetParser "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM"using PPM mass differenceWARNING: Cannot non-parametric distributions without decoys! (MS-GF+)WARNING: Support of MSGF+ may not be full. There exist known issues with the way MSGF+ encodes certain modifications in pep.xml that may not be correct. Also, high-scoring DECOY have been observed in MSGF+ analysis. The user is encouraged to be vigilant in comparing model estimated error-rates to the DECOY-estimated error-rates to make sure the two agree and set CLEVEL parameter accordingly: see http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#What_is_CLEVEL_and_when_do_I_use_it.3FWARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search.WARNING: MSGFPL only support semi-parametric PeptideProphet modelling, which relies on a DECOY search. init with MS-GF+ trypsin MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN INFO: Processing standard MixtureModel ... PeptideProphet (TPP v5.1.0 Syzygy, Build 201711031215-7670 (Windows_NT-x86_64)) AKeller@ISB read in 0 1+, 6282 2+, 5137 3+, 1488 4+, 0 5+, 0 6+, and 0 7+ spectra. Initialising statistical models ... Iterations: .........10.........20 command "C:/TPP/bin/PeptideProphetParser "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM" failed: Unknown error command "C:/TPP/bin/PeptideProphetParser "/tmp/a02972/params/MS-GF/interact.pep.xml" MINPROB=0.05 PPM NONPARAM" exited with non-zero exit code: -1073741819 QUIT - the job is incomplete Could anybody please help me out to fix this problem. Thanks. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. 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